The Lost Resistance
by Flexis
Summary: The year is 2037. Colonization has already destroyed the Earth. Mulder and Scully, who were frozen until this year, return to Earth to find the world has changed...as well as people they once knew. (It has been edited for fanfic.net) please r&r. COMPLETED
1. 35 year slumber

Prologue

He made love to the cloudy eyed female. He didn't even know her name. He sent her out of the room after she collected her clothes. He got up and pulled his garments on just as a sharp knock sounded at the door.

"Enter" he barked, raking a hand through his auburn hair. The door slid open and Marcus, his adviser, walked in.

"Sir, more have been captured. What do you wish to do with this bunch?" Marcus asked, handing the disregarded garments to his King.

"I'll be there shortly to speak with them," he replied. Marcus nodded and walked briskly to the door. "

Oh, and Marcus?" Marcus stopped short.

"Yes, my King?".

"Make sure they are fed."

Marcus bowed his head and left the room.

Chapter 1

He held her hand tightly, searching her blue eyes. She bit her lower lip and leaned into him. He welcomed the embrace and kissed the top of her head.

"It will be ok" he whispered. To her it sounded more like a question than a statement.

Her mind raced with uncertainty as he broke the embrace and led her down the cold hall. They entered the room and each laid on an examination table. Krycek stood in the corner, holding Mulder's gaze.

"You are doing the right thing Mulder." Mulder turned his head to the other corner of the room where the Lone Gunmen stood. They smiled their encouragement.

Scully nervously tucked a strand of hair behind her ear. She looked at Mulder and followed his gaze to the empty wall across the room.

"Mulder", she whispered. He looked at her with tears in his eyes. His heart thumped wildly. They stared held each other's gaze until the doctors entered the room.

They went to her first and she swallowed back a sob as they slid the needle into her arm. He watched her eyes roll into the back of her head as a sharp pain stuck his arm. Everything went black.

A Doctor shook his head at the scenario. "Thirty-five years", he muttered, shaking his head. He helped the team move the couple to the cryo-cubaters. He prayed to the heavens that this worked.


	2. Fight the Future

Chapter 2

"Scully…Scully…Scully."

"He's coming to"

"I'm right here Mulder"

"SCULLY!," Mulder howled her name, shooting upright. His eyes slowly focused on the faces that stood around him. Scully stood next to him, her hand stroking his. Several men that appeared to be doctors were standing all around him. He saw worry and curiosity in each of their eyes. His mind tried to make sense of what was happening. His mind worked furiously, spurting out images that wouldn't slow down. Holding Scully, watching her weep, leaving with Skinner, the ship. Oh God, the ship.

"What year is it?" he asked groggily. Scully's grip tightened on his hand as if to balance herself.

"Um, that would be 2037 sir," a young doctor stated. A whimper escaped Scully's lips.

"It worked," Mulder breathed. Scully swayed and fell suddenly to the floor. The doctor's rushed to her aid and set her back onto a table.

"That's the third time." Krycek chuckled. Mulder jumped at his sudden presence.

Mulder ignored him and slid off the table. "How do my legs work after being asleep for thirty-five years?" Mulder asked, not really expecting an answer.

"Well sir, while you underwent oxygenated fluorocarbon emulsion there were electric shocks sent to your muscles which kept them in the same condition that they were in before. You are the exact height, weight, and in a sense…age," the same boy answered. Mulder stared at the boy wondering what it was about him that looked so familiar. He reminded himself that any familiar faces to him were now faces in the past, faces that wouldn't exist anymore.

The young man smiled and said, "I'm Walter Skinner's son. My name is Trent."

Another doctor interjected, this one a woman, "Actually Mr. Mulder, you'll find that most of the people that you come into contact with here are related to those that you knew." Mulder sat back down and swallowed a lump that was forming in his throat.

"So you would be?" he asked the woman.

She smiled and replied, "Leslie Doggett. My mother and father are anxious to see you two."

As if on cue, John Doggett entered the room with Monica at his side. She immediately went to a now waking Scully. Mulder noted that they looked older but not old enough to be in their 70's.

Trent picked up on his confusion and said, "They didn't age the same as us kids. They were in space a very long time." His voice sounded far away and his eyes grew thoughtful.

"Your father, where is he?" Mulder asked.

Trent cleared his throat and looked at the ground. The room fell silent. "He is still out there somewhere. A huge chunk of the resistance boarded a rebel alien ship to leave Earth to plan on how to take out the other aliens. It is the same ship that your bodies lived in. He came and talked to you often. The ship…was attacked and only some escaped back to Earth."

Mulder looked at Scully who was holding Monica's hand tightly. She looked back at him and he saw a shift in her expression. She looked ready to get up and fight. His heart swelled and he found the buried fight within him.

Krycek's hand grasped Mulder's shoulder and his whisper filled his soul, "Fight the Future".


	3. Memories

Chapter 3

He watched her pull her long hair into a bun. She felt his eyes on her and she turned to see him staring contently at her.

"Do they have a hair salon in this place?" she joked, tugging at her extremely long red locks.

"I think I like the Repunzel look Scully" he replied, stretching his arms above his head. She smiled a half-hearted smiled and carried a bag she had packed thirty-five years ago to the bed. Mulder leaned over so that he could see what was in it. She pulled out her's and Mulder's guns and set them on the bed. She then pulled out her cross necklace and a tear fell down her cheek. He took it from her and fastened it around her neck. She touched the cross lightly and smiled through tears at Mulder. He touched her cheek and then looked at the bag, urging her to continue. She pulled out Mulder's clothes and then her own. At the very bottom she felt a thin, glossy paper. She slowly pulled it out and stared into the eyes of her son. She let it fall into her lap and her face went into her hands as her body retched with sobs. Mulder picked up the picture and looked at it, his hand shaking slightly.

"I've seen him you know" came Kryceks voice. Mulder looked up to see him standing at the door.

"He looks just like her..and you". Mulder threw the empty bag at Krycek, watching it hurl right through his body. He was in no mood for games, especially not ones dealing with his son.

Scully looked at him, wondering why the sudden outburst. He touched her cheek and got off the bed. He stood with his back to her and tried to collect his thoughts. William was alive. They were underground. Where was William? How many people were left…real people? What did the world look like now? It must be bad up there. His thoughts were interrupted when he felt her small but strong hand on his back. He turned around and she handed him his clothes. They dressed in silence with their backs turned to each other.


	4. Resist or Serve

Chapter 4

Scully hadn't realized how large this underground facility was. It housed 21 colonies. The only real humans left in the world. She walked with Monica to the dining area where she saw that Mulder was already sitting with Trent, John, and Leslie.

Before reaching the table Scully whispered to Monica, "Leslie is beautiful. She really got the best out of you and John." Monica beamed and squeezed Scully's hand.

Scully took her seat next to Mulder and it was near silent as their food was brought to them by various members of the colony. A woman with big blue eyes set her's and Mulder's food in front of them. The woman reminded Scully of Melissa which brought another twinge of pain to Scully's heart.

"So I suppose we all have a lot to tell you and you have a lot to learn before we get started." John said as everyone nibbled at their food.

Scully and Mulder listened as John, with help from Monica, Trent, Leslie, and some others, told them about how the aliens came quickly. Most died from bee stings and the aliens that hatched out of the human bodies were taken away on their ships, unclear where to. Many people's bodies remained on the Earth, but their souls were long gone, the aliens taking their form as these people. They wouldn't see the same aliens that Mulder came into direct contact with in Antarctica. They would see people whose eyes turned black. The world was overcome by a mix of humans and aliens. Some were aliens that took control of human bodies, other's were half human DNA half alien DNA.

Mulder could no longer swallow his food. His mind was racing. "The alien-human race…they are hostile?" he asked.

John hesitated before answering. "They are kinder than the aliens themselves. You see, the alien-humans, Kinliens we like to call them, were formed by our government along with theirs a long time ago. This was all planned. To use those who wouldn't cooperate as hosts for the aliens and then breed aliens and humans together to make a bettered race for humankind. Some were bred, others were made by means of being injected with the tampered DNA. It was either that or have all humans killed off completely. This way, the families of all of the government's group would live on and the aliens could produce more of their own kind. These Kinliens posses powers that we have seen before."

"Gibson" Scully whispered.

John nodded.

"William" Scully said again. There was a long moment of silence.

"So what do we do? We kill them? We kill what is half us?" Scully asked, only William in her mind.

"They kill groups of the resistance every day." Monica said softly.

"What is it that we must do?" Mulder asked.

"Resist or Serve" krycek hissed in his ear.


	5. I Want to Believe

Chapter 5

Mulder and Scully sat in John's office. He and Monica were trying to fill them in on how they usually went about getting to the Kinlien Colony. They explained that the Earth looks nothing like it used to. The cities are gone, houses gone. Nothing but nature was left. There was only the one city. The city of the Kinliens. The Resistance colonies were underground very close to the Kinlien city. They set up teams that would travel as far as they could into the city. They would never get too far because these Kinliens were able to read human minds with ease. They could sense the presence.

"I'm not understanding John. We want to kill them or negotiate with them? What is the point here?" Scully asked.

"We would like to live in peace, of course Dana" Monica said.

John interrupted her, "But they never let us get close enough to talk to them. The ones that we have lost we have never seen or heard from again. We fear the worst. You were brought to this year in your age for a reason. You are the only ones that can get into that city and talk with their king."

"Their King?" Mulder asked, his question dripping with disgust and slight humor. Monica and John exchanged glances.

"Why can we only get into the city?" Scully asked, her brows knit together.

"They cannot kill their own." John answered hesitantly.

"Their own?…Just spit it out Doggett." Mulder exclaimed.

Scully gasped, her eyes wide. She grabbed Mulder's arm. "Mulder, William is their king." Mulder jumped slightly at the realization.

John and Monica let the information settle with Mulder and Scully before prompting on. "We believe…the whole colony believes that you two are our last and only hope" Monica said softly, taking each of their hands in her own.

"When do we go to him?" Scully asked.

"Whenever you are ready but, the sooner the better," John replied.

The next few hours were filled with excitement and tension in the colonies. News of Mulder and Scully's departure was sent on everyone's ears. They would leave with a crew containing Trent, Leslie, and two other members of the colony. The other two, named Tess and Hank would be the eyes and ears of the operation while Trent and Leslie would provide protection at all times for Mulder and Scully.

A large banquet was held to say goodbye and good luck to the two former agents. Mulder looked embarrassed by all the hoo-ha while Scully looked preoccupied in her own thoughts.

Mulder followed the team out of the banquet room with Scully behind him. She felt a tug at her shirt and she turned around to see a small boy with big green eyes and chubby cheeks stare up at her.

Scully smiled and squatted so that the child could lean and whisper into Scully's ear, "We want to believe"


	6. Trust Someone

Chapter 6

The night sky was beautiful. It was the only familiar thing in their surroundings. It looked like Earth, it felt like Earth, but it just wasn't the same. It felt like a foreign planet, but that most likely was because it was over run by an alien being, Scully mused.

She watched Mulder talk with Trent quietly as they trudged through the thick forest behind Hank and Tess. Leslie stood next to Scully, her eyes scanning to forests and her gun held steadily in her hands. Scully smiled at how much she resembled Monica. Except for the sharp slanting eye shape she inherited from John, Leslie could not have been mistaken as any other's daughter.

Leslie noticed Scully's gaze and she smiled shyly at Scully. "My mother and Walter would always entertain me and Trent with their stories of you and Mulder. They told us about the monsters in the X files and what a good friend you were."

She looked down before she continued. "Before my parents and Walter went back on the ship that you two were held on, William was here. We were friends. He was taken from us when he was 10 by the aliens. He knew the stories about you too, but he never knew…he never knew you were his parents. He thought that Walter was his father. He never told him he was or that he wasn't. Trent of course thinks of William as his brother. He misses him very much. We all do." Leslie glanced at Scully to see her crying.

"I'm sorry." Leslie mumbled.

Scully shook her head vigorously. "No, it is ok. Wha-..what was he like?" Scully asked.

Leslie smiled and looked up at the sky as if trying to pluck her memories out of the heavens. "He was shy with strangers. Well, I always thought him shy, but Walter said he was like his father in that area…a loner, withdrawn, an analyzer. He was so smart and kind as well. Trent would be bossy with him and William would just see that that was the way Trent was and let him boss him around, knowing that it wouldn't matter later on. He loved to explore. He had to know where everything was and everything about anything. He would make up these adventures for Me and Trent to partake in. His favorite was Moby Dick. That was his favorite book. He would always let Trent be Ahab though I knew William made a better Ahab." Leslie stopped when Scully's crying became more evident.

Mulder turned his head to see Scully crying. Trent stopped with him and they all stood in the dark and quiet forest, taking a break.

"I'm sorry, it is my fault. I was telling her what I remembered about William." Leslie admitted. Trent gave her a stern glare and he clenched his jaw. He didn't like to be reminded of William.

Mulder held Scully much to her dismay. "I'm fine, stop it Mulder, I'm fine!" she exclaimed, pushing him away.

Just then a tree branch snapped and they all whirled around to see six guns pointed at them. "Come with us and we will not shoot," one of them said.

They all walked with their hands up in the air and with guns lodged into their backs the remainder of the way. Scully and Mulder's breath caught in their throats when they got to the city. It was beautiful. It reminded Scully of the Elvin city in _The Lord of the Rings_. They were walked through the city, Kinliens stared and probed their minds. Most would not make eye contact. They were thrown into a large cell that reeked of urine and vomit.

"Nice town, friendly folk", Mulder commented. Scully snorted and folded her arms nervously.

"What now?" Scully asked.

"We wait", Trent answered.

Leslie reminded the group, "Try not to think about William or our relations with him. We don't want anyone knowing before he does."

They all nodded, all thinking about how near impossible that would be. Scully tried not to cry again. Their son, the product of half of Mulder and half of herself was the one thing she feared the most.

It was hours before they were released and taken into what looked like the main structure of the city. They were seated at a long, fancy table and served food. They ate warily, not daring to speak. Guards lined the walls, staring blankly at the prisoners. Mulder put a shaking hand on Scully's knee under the table. She relaxed slightly, reminding herself that Mulder was by her side. Whatever was to come, they would go through it together.

The door opened abruptly, causing everyone to give a slight jump. A man walked in, a bored expression on his face and he stood by the door. "Your King", the man stated holding his arm out. If Mulder wasn't so nervous he would have laughed his ass off at the statement. Scully's hand found his under the table and her grip caused his fingertips to pulse.

A man strolled in, patting the man at the doorway on the shoulder.

"Thank you Marcus, that will be all", he told him.

His body was a spitting image of Mulder's from the lean middle up to the broad shoulders. His hair was the dark brown of Mulder's with a hint of red dispersed throughout it. His face held many of the soft features of his mother. He held her sharp nose and delicate cheek bones but he had his father's strong jaw line and dimpled chin. His eyes were the part that made Scully's heart jump. It was like looking into her own except they weren't the clear blue. They were the hazel pools of color that she had grown to know so well in Mulder's eyes. He was beautiful.

He walked slowly to the table and pulled out a seat for himself, looking at each of their faces. Scully's lip quivered when their gazes met. Out of the corner of her eye she could see Mulder's jaw clenching and unclenching.

"Hello William", Trent murmured. William smiled a small smile that reminded Mulder of Scully's amused grin she often displayed while working on the X files.

"Hello Trent. How is father?" William asked, leaning forward eagerly.

"He's gone." Leslie answered for him. William looked at her, his face softening. "Leslie", he whispered. She wouldn't look him in the eye.

He then looked at Mulder and Scully, trying to figure out who they were. Then his face broke into a slight smile and he stated, "Ah, and you must be the famous Mulder and Scully I heard so much about as a child." Scully looked down at her hands, emotions too strong to comprehend.

Mulder cleared his throat and said, "I didn't realize we were famous enough for the ears of a King."

William's eyebrows knitted together in the same fashion as his mother's and he softly replied, "Father had many things to say about you. I knew one day you would come here. You are the King of the resistance. This day was destined to happen. I have waited many years."

Scully looked up and caught her son's eyes. She could feel him pull into her mind and she tried hard not to let the picture of her baby William enter her mind. He could sense her fear and her pain. He could sense her loss. _You need not be afraid_. He told her in her mind. She nodded and looked away.

"William. You must know why we are here. Our people die everyday. We just want peace. We want to exist." Leslie prodded.

William reached across and took her small hand in his. "I have missed you so much Leslie. I think about you daily." William told her, his eyes solemn. She took her hand away as if he stung her.

The hurt was evident on his face. "I cannot promise you anything. You know I can't do that. I can promise your safe return out of the city." He told her.

"We want peace." Trent stated harshly.

Williams face flashed in anger and he got up from the table, his chair knocking over. "Why do you come asking for impossible things of me? Why do you come now. Why not earlier. Why do you burden me with all of this? You know I cannot." He seethed, pacing the room.

Leslie started to cry. Trent got out of his chair as well and got into William's face. "You are no King! You are as human as I! You are a coward William! You sit up here in your little palace instead of with your family, fighting for our existence."

William's jaw clenched as his eyes had a silent war with Trent's. Finally he broke the glance and said very low, "I have no one. I trust no one. I have no family. I have no one to live for except myself. I am no human. I am not like you Trent. Or you Leslie."

Leslie got up and walked to William. She put her hand on his arm and pulled him to her. He leaned into her embrace and her fingers kneaded through his hair. "Will, you have me. You ARE human. You are different but human. You had a mother and a father. You were a miracle. You are loved. Please. Please save us." Tears streamed down her face.

William pushed her away and looked angrily into her eyes. "What mother? What father? What human can do this?!" with one look he threw a chair against the wall and he entered each of their minds simultaneously; _now tell me I am human_.

Scully lifted herself out of the seat. Leslie and Trent sat down, understanding what events were to occur. She walked over to William and put her hand on his cheek. He looked at her, the confusion evident on his face. She looked deep into his eyes, willing him to enter her mind. His eyes fluttered closed and his mind filled with images of a kiss between Mulder and Scully, Monica yelling at Scully to push, Scully holding a baby in her arms screaming at a group of people to get away from her baby, Mulder smiling down at the bundle in Scully's arms, Scully kissing the baby's forehead before putting him in Skinner's arms, Scully crying alone on her kitchen floor with a baby blanket clutched in her hands. His eyes shot open and he saw the tears streaming down her face. Her chin wrinkled under the pressure of her concealed sobs. He touched her cheek as well and his thumb traced small circles on her cheek bone.

Mulder got up and came up behind Scully. He put a hand on her shoulder and looked into his son's eyes for the second time in his life. "So the king of the alien race is the spawn of the king of the resistance" William stated. He let his hand drop from Scully's face and he looked down at his feet, trying to collect his thoughts.

"I will help you then. I will leave the colony and join with yours. There will never be peace. They will never understand why I leave so I will not try to explain or justify my reasoning. They will be lost and angry without me. I believe I'll put you in more danger if I leave but I cannot stay and know that my enemy is my family. I have gone too long without family." William said, his eyes switching gazes between Mulder and Scully. Leslie came up behind William and threw her arms around his waist. He turned around and hugged her tightly. Trent beamed and whispered, "Welcome back, brother."

"Is my sister well? Does she hate me?" William asked.

"Your sister?" Scully asked in confusion.

William frowned and replied, "Well yes, Emily."

Scully gasped and her mind immediately flew back to the woman's face that served hers and Mulder's food that first night. The one that looked so much like Melissa.

"We have to hurry. They will hear our thoughts. We cannot make any plans until we are far from them all", William said. Krycek appeared in front of Mulder. He was smiling a cocky smile and said, "Remember Mulder, trust no one."

Mulder smiled back and whispered, "But I can trust my son"


End file.
